GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Desulfovibrio vulgaris Miyazaki F

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__Miya:8499890
          Length = 350

 Score =  273 bits (698), Expect = 5e-78
 Identities = 152/358 (42%), Positives = 222/358 (62%), Gaps = 23/358 (6%)

Query: 1   MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60
           M+++QL NV++ WG+V    D++ ++ +G  +V +GPSGCGKST LR+IAGLE++TSG +
Sbjct: 1   MSAIQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60

Query: 61  FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120
            IGE+ +   PPA+R + MVFQSYAL+PHL+V EN+ FGL +    +    +R+ +  ++
Sbjct: 61  MIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDI 120

Query: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180
           L L+ LL RKP  LSGGQ+QRVA+GR LVAE +V L+DEPLSNLDA LR +MR EI  L 
Sbjct: 121 LGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQ 180

Query: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240
           + LG TM+YVTHDQ EAM++AD+I+++  GR+ Q   P ELY  PA  F   FIG+P MN
Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPMN 240

Query: 241 FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVIL 300
            +        +D  +  + +   +   + V        A+  LGIRPEH+       ++ 
Sbjct: 241 LV-------RLDDARGSVCVAGSRSGTVSVVD-----SADYVLGIRPEHI------RIVP 282

Query: 301 EG---EVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLF 355
           EG    V+ VE LG+ + +  ++     ++V   + V  +  GA   +  P E  H+F
Sbjct: 283 EGWRAVVESVEYLGSGSVLGCRVGGEELSVVV--DGVPTIAVGAEIYLHCPDEHIHIF 338


Lambda     K      H
   0.320    0.137    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 309
Number of extensions: 7
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 371
Length of database: 350
Length adjustment: 29
Effective length of query: 342
Effective length of database: 321
Effective search space:   109782
Effective search space used:   109782
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory